1. 讲 座 提 纲讲 座 提 纲 1 什么是分子育种 2 历史回顾 3 全基因组策略 4 基因型鉴定 5 表现型鉴定 6 环境型鉴定 (etyping) 7 标记 - 性状关联分析 8 标记辅助选择 9 决策支撑系统 10 展望

2. whole genome sequencing targeted region sequencing whole genome/targeted region resequencing SVs, SNP identifying, Exome sequencing DNA methylation, Studying gene regulation mRNA, ncRNA, small RNA, miRNA, regulatory RNA Gene expression Finding genes whole transcriptome shotgun Protein-DNA ChIP on Sequencing Metagenomics

3. Human Genome Sequence 200320082012 Time (start to finish)13 years4.5 months1 day Cost (start to finish)$ 2.7 billion< $1.5 million< $ 5000 Development of Sequencing Technology

4. Pedigree Genotype Phenotype Environmental factors Genome Metablome Transcriptome Proteome Pathways Networks Air Light Humidity Temperature Mechanical Nutrients Water Pathogens Symbionts

5. Data Tsunami - Examples Genotype data Kb level: All available germplasm Maize (27,000 accessions, CIMMYT) Wheat (148,000 accessions, CIMMYT Rice (113,000 accessions, IRRI) Mb level: Marker X Accessions 10K X 100K for variety protection & MAS 50K X 100K for genetic diversity 2-5M X 10K for GWAS (maize) Tb level: Omics data DNA sequence Resequencing 100 maize inbreds at 10X 100 inbreds X 10X depths X 2.5Gb =2.5Tb RNA sequence Protein sequence

6. Breeders need help with breeding informatics tools to get out of the data tsunami Breeder Bioinformatics and Computing Are Needed in Plant Breeding We need to work together to make this happen Revised from Gary Atlin

7. Super Computation Platform Integration of Information of Multiple Sources Genotypic data from large numbers of accessions/ individuals across populations and germplasm collections Phenotypic data collected worldwide and multi-location trials for the genotyped accessions/individuals Environmental data collected from the environments where the phenotyping is performed

8. G-P-E Information Collection Information Integration Data standardization Development of generic databases Use of controlled vocabularies/ontologies Interoperable query system Redundant data condensing Database integration Tool-based information integration Information retrieval and mining Information management systems Breeding Informatics

9. 66% Missing data rate: 2% Missing data rate: Missing Data Imputation and Haplotype Analysis I II III Average accuracy: ~98% (based on four sets of BACs-based sequences and high-coverage sequence data for quality control)

10. G-P-E Germplasm management, evaluation, and enhancement Breeding population management and improvement Building up heterotic patterns Prediction of hybrid performance Marker-assisted inbred and synthetic creation Genetic map construction Marker-trait association identification and validation Marker-assisted selection methodologies and implementation Genotype by environment interaction analysis Intellectual property right and plant variety protection Breeding design through simulation and modeling Decision Support Tools Xu 2010 Molecular Plant Breeding. CABI

11. G enotype Sequences Markers Maps Genealogy P henotype Yield Quality Agronomy Stress response E nvironment Water Fertilizer Soil Temperature Precipitation GIS Day length DataTools Output Gene functional analysis Genetic diversity Germplasm evaluation Germpalsm classification Variety identification Genetic mapping Marker-trait association Marker-assisted selection GXE interaction Environmental classification Variety stability/adaptability LIMS and Analytical Tools for Genetic Improvement BLASTN/X… Mapmaker MultiQTL GeneFlow QTL Cartographer SAS/JAMP Structure GeneMapper PowerMarker Arlequin BiPlot CMTV TASSEL …….. Integrated IMS for molecular breeding ICIS Xu 2010 Molecular Plant Breeding. CABI

12. Integrated Breeding Platform (IBP) https://www.integratedbreeding.net/ A web-based, consolidated vehicle for dissemination of knowledge, tools and services, enabling broad access to and proactive distribution of Crop information and breeding material Molecular, genomics and informatics technology Cost-effective high-throughput genotyping services Capacity-building programs to design and carry out crop breeding projects Coordinated by the Generation Challenge Programme of the CGIAR.Generation Challenge ProgrammeCGIAR

13. IBP provides tools to help breeders in designing experiments managing experiments collecting data storing data conducting analyses The tools are available for download as a single consolidated application – the Integrated Breeding Workflow System (IBWS).Integrated Breeding Workflow System More information from Gary Atlin and Jean-Marcel Ribaut (2014)